Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_013403646.1 CALHY_RS08990 FAD-dependent oxidoreductase
Query= BRENDA::Q76M76 (483 letters) >NCBI__GCF_000166355.1:WP_013403646.1 Length = 420 Score = 146 bits (368), Expect = 2e-39 Identities = 110/326 (33%), Positives = 166/326 (50%), Gaps = 16/326 (4%) Query: 118 KADVVVIGGGPAGLMAAIHAADA--GASVILIDENPMLGGQLVKQTHKFFGKREQFAGVR 175 K VVVIGGGPAGL AA+ + + V++I+ + LGG L + H FG + Sbjct: 3 KYKVVVIGGGPAGLAAALESFKSLDDKKVLIIERDKFLGGILNQCIHPGFGLHYFKEELT 62 Query: 176 GVKIAEILGEEVKKRGNIEVFLETSAVGVFHEGEEKLVAAVRKNKELLEFLGKTLVVATG 235 G + A E+V + IE ET + + E E + AV K K L ++V+A G Sbjct: 63 GPEYAHRFVEQVVEN-RIEYLTETHVIDITPEKE---IVAVNK-KGLKRIKADSIVLAMG 117 Query: 236 AMEKM---IPFENNDLPGIYGAGAIQTLMNTYGVKPGDRVLIVGAGNVGLILAYQLIQAG 292 E+ I GI+ AG Q +N G + G + +IVG+G++GLI+A +L G Sbjct: 118 CRERTRGAIITPGTRPAGIFTAGQAQRFINIEGYRIGKKAVIVGSGDIGLIMARRLTLEG 177 Query: 293 VEVKAIVEAMPKVGGYFVHAAK-VRRLGVPILTRHTILRAEGKDRVERAVIAQLDENWRP 351 +EVKA+VE MP G + + + G+P+L H +++ GK RVE IA++D + Sbjct: 178 IEVKAVVEIMPYSTGLRRNIVQCLDDFGIPLLLSHKLVKIHGKYRVEGVTIAKVDSQLQE 237 Query: 352 VPGTEKVFEVDTIALAVGLRPSIELLHQAGCQVKFVRELSGHVAVRDGRMETTVQGIFVA 411 +P TE+ E DT+ +VGL P EL +AG V ++ V D T+ +GIF Sbjct: 238 IPSTERFIECDTVLFSVGLIPENELSKKAG----VVLDMRTGGPVVDNTFSTSQKGIFAC 293 Query: 412 GDSAGIEE-ATTAMLEGKIAGIAAAL 436 G+ + + LE + AG AA+ Sbjct: 294 GNVLHVHDLVDNVTLEAQTAGRYAAI 319 Lambda K H 0.319 0.138 0.397 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 460 Number of extensions: 25 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 483 Length of database: 420 Length adjustment: 33 Effective length of query: 450 Effective length of database: 387 Effective search space: 174150 Effective search space used: 174150 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory